diff --git a/communities/biodiversity/resources/curated_tools.tsv b/communities/biodiversity/resources/curated_tools.tsv new file mode 100644 index 000000000..9061745ee --- /dev/null +++ b/communities/biodiversity/resources/curated_tools.tsv @@ -0,0 +1,133 @@ +Galaxy wrapper id Galaxy wrapper id Galaxy tool ids To keep Deprecated +TrimNs TrimNs trimns FALSE FALSE +abacas abacas abacas FALSE FALSE +abyss abyss abyss-pe FALSE FALSE +assembly-stats assembly-stats assembly_stats FALSE FALSE +assemblystats assemblystats assemblystats FALSE FALSE +bam2mappingstats bam2mappingstats bam2mappingstats FALSE FALSE +bionano bionano bionano_scaffold FALSE FALSE +biscot biscot biscot FALSE FALSE +cap3 cap3 cap3 FALSE FALSE +combine_assembly_stats combine_assembly_stats combine_stats FALSE FALSE +fastk fastk fastk_fastk FALSE FALSE +filter_spades_repeats filter_spades_repeats filter_spades_repeat FALSE FALSE +flye flye flye FALSE FALSE +getorganelle getorganelle get_annotated_regions_from_gb, get_organelle_from_reads FALSE FALSE +graphmap graphmap graphmap_align, graphmap_overlap FALSE FALSE +hapcut2 hapcut2 hapcut2 FALSE FALSE +hapog hapog hapog FALSE FALSE +hifiasm hifiasm hifiasm FALSE FALSE +hisat hisat hisat FALSE FALSE +hisat2 hisat2 hisat2 TRUE FALSE +hypo hypo hypo FALSE FALSE +idba_ud idba_ud idba_hybrid, idba_tran, idba_ud FALSE FALSE +instagraal instagraal instagraal FALSE FALSE +jellyfish jellyfish jellyfish FALSE FALSE +links links links FALSE FALSE +merqury merqury merqury, merquryplot FALSE FALSE +meryl meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode FALSE FALSE +minia minia minia FALSE FALSE +miniasm miniasm miniasm FALSE FALSE +mitobim mitobim mitobim FALSE FALSE +mitohifi mitohifi mitohifi TRUE FALSE +necat necat necat FALSE FALSE +nextdenovo nextdenovo nextdenovo FALSE FALSE +novoplasty novoplasty novoplasty FALSE FALSE +plasmidspades plasmidspades plasmidspades FALSE FALSE +promer promer promer4_substitutions FALSE FALSE +purge_dups purge_dups purge_dups FALSE FALSE +quast quast quast FALSE FALSE +quickmerge quickmerge quickmerge FALSE FALSE +ragtag ragtag ragtag FALSE FALSE +raven raven raven FALSE FALSE +salsa2 salsa2 salsa FALSE FALSE +shovill shovill shovill FALSE FALSE +smudgeplot smudgeplot smudgeplot FALSE FALSE +taxonomy_krona_chart taxonomy_krona_chart taxonomy_krona_chart TRUE FALSE +tgsgapcloser tgsgapcloser tgsgapcloser FALSE FALSE +trycycler trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample FALSE FALSE +unicycler unicycler unicycler FALSE FALSE +velvet velvet velvetg, velveth FALSE FALSE +velvet_optimiser velvet_optimiser velvetoptimiser FALSE FALSE +verkko verkko verkko FALSE FALSE +wtdbg wtdbg wtdbg FALSE FALSE +yahs yahs yahs FALSE FALSE +seq_filter_by_mapping seq_filter_by_mapping seq_filter_by_mapping FALSE FALSE +sample_seqs sample_seqs sample_seqs FALSE FALSE +seq_primer_clip seq_primer_clip seq_primer_clip FALSE FALSE +flash flash flash FALSE FALSE +shasta shasta shasta FALSE FALSE +khmer khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median FALSE FALSE +clc_assembly_cell clc_assembly_cell clc_assembler, clc_mapper FALSE FALSE +samtools_idxstats samtools_idxstats samtools_idxstats FALSE FALSE +blastparser_and_hits blastparser_and_hits BlastParser_and_hits FALSE FALSE +oases oases oasesoptimiserv FALSE FALSE +rnaquast rnaquast rna_quast FALSE FALSE +spades spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades FALSE FALSE +count_roi_variants count_roi_variants count_roi_variants FALSE FALSE +coverage_stats coverage_stats coverage_stats FALSE FALSE +samtools_depad samtools_depad samtools_depad TRUE FALSE +samtools_depth samtools_depth samtools_depth TRUE FALSE +fermikit fermikit fermi2, fermikit_variants FALSE FALSE +EMLassemblyline EMLassemblyline eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template FALSE FALSE +Ecoregionalization_workflow Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker TRUE FALSE +Geom_mean_workflow Geom_mean_workflow Map_shp, Mean_geom, bar_plot FALSE FALSE +PAMPA PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm TRUE FALSE +aquainfra_importer aquainfra_importer aquainfra_importer FALSE FALSE +champ_blocs champ_blocs cb_dissim, cb_ivr, cb_div TRUE FALSE +data_exploration data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs TRUE FALSE +dose_responses dose_responses dr_curve FALSE FALSE +gdal gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo TRUE FALSE +hirondelle_crim_ogc_api_processes hirondelle_crim_ogc_api_processes hirondelle_crim TRUE FALSE +interpolation interpolation interpolation_run_idw_interpolation TRUE FALSE +obisindicators obisindicators obisindicators, obis_data TRUE FALSE +ocean ocean argo_getdata FALSE FALSE +ogcProcess_otb_bandmath ogcProcess_otb_bandmath otb_band_math FALSE FALSE +ogcProcess_otb_meanShiftSmoothing ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing FALSE FALSE +regionalgam regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend TRUE FALSE +retrieve_bold retrieve_bold retrieve_bold TRUE FALSE +sdmpredictors sdmpredictors sdmpredictors_list_layers TRUE FALSE +spocc spocc spocc_occ TRUE FALSE +srs_tools srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata TRUE FALSE +stoc stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic TRUE FALSE +vigiechiro vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid TRUE FALSE +xarray xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select FALSE FALSE +zoo_project_ogc_api_processes zoo_project_ogc_api_processes zoo_project_ogc_api_processes TRUE FALSE +medenv medenv iabiodiv_smartbiodiv_med_environ TRUE FALSE +baseline_calculator baseline_calculator tt_baseline FALSE FALSE +annotatemyids annotatemyids annotatemyids FALSE FALSE +biotradis biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites FALSE FALSE +braker braker braker FALSE FALSE +braker3 braker3 braker3 FALSE FALSE +deepsig deepsig deepsig FALSE FALSE +funannotate funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort TRUE FALSE +goenrichment goenrichment goenrichment, goslimmer FALSE FALSE +helixer helixer helixer FALSE FALSE +icescreen icescreen icescreen FALSE FALSE +pharokka pharokka pharokka FALSE FALSE +prodigal prodigal prodigal FALSE FALSE +repeatexplorer2 repeatexplorer2 repeatexplorer_clustering FALSE FALSE +repeatmodeler repeatmodeler repeatmodeler FALSE FALSE +telescope telescope telescope_assign FALSE FALSE +transit transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps FALSE FALSE +tsebra tsebra tsebra FALSE FALSE +chipseeker chipseeker chipseeker FALSE FALSE +disco disco disco FALSE FALSE +circexplorer2 circexplorer2 circexplorer2 FALSE FALSE +blast_to_scaffold blast_to_scaffold blast2scaffold FALSE FALSE +blastx_to_scaffold blastx_to_scaffold blastx2scaffold FALSE FALSE +blobtoolkit blobtoolkit blobtoolkit FALSE FALSE +ear ear make_ear FALSE FALSE +megahit megahit megahit FALSE FALSE +megahit_contig2fastg megahit_contig2fastg megahit_contig2fastg FALSE FALSE +metaeuk metaeuk metaeuk_easy_predict FALSE FALSE +spaln spaln list_spaln_tables, spaln FALSE FALSE +taxonomy_filter_refseq taxonomy_filter_refseq taxonomy_filter_refseq TRUE FALSE +extract_ipm_date_interval extract_ipm_date_interval FALSE FALSE +insect_phenology_model insect_phenology_model FALSE FALSE +test test FALSE FALSE +validate_temperature_data validate_temperature_data FALSE FALSE +gdal gdal TRUE FALSE +mean_per_zone mean_per_zone FALSE FALSE +netcdf_handler netcdf_handler TRUE FALSE +run_idw_interpolation run_idw_interpolation FALSE FALSE \ No newline at end of file